If you are familiar with Docker containers, Singularity/Apptainer containers are essentially the same thing, but are better suited for multi-user HPC systems such as LUMI. The main benefit of using a container is that it provides an isolated software environment for each application, which makes it easier to install complex applications.
This page provides guidance on preparing your Singularity/Apptainer containers for use with LUMI. Please consult the container jobs page for guidance on running your container on LUMI.
Building containers for LUMI¶
Building containers on LUMI is, unfortunately, not an option; The
build command requires some level of root privileges, e.g.
fakeroot, which are disabled on LUMI for security reasons. Thus, in order to
prepare a Singularity/Apptainer container for LUMI, you have two options:
- Pull an existing container image (Singularity or Docker) from a registry.
- Build your own container on your local hardware, e.g. your laptop.
Pulling container images from a registry¶
Singularity allows pulling images (Singularity or Docker) from container
registries such as DockerHub or AMD Infinity Hub.
Pulling container images from registries can be done on LUMI. For instance, the
ubuntu:22.04 can be pulled from DockerHub with the following
This will create the Singularity image file
ubuntu_22.04.sif in the directory
where the command was run. Once the image has been pulled, the container can be
run. Instructions for running the container may be found on the container jobs
Please take care to only use images uploaded from reputable sources as these images can easily be a source of security vulnerabilities or even contain malicious code.
The compute nodes are currently not connected to the internet. As a consequence, the container images need to be pulled in on the login nodes (or transferred to LUMI).
When pulling docker containers using singularity, the conversion can be
quite heavy. Speed up the conversion and avoid leaving behind temporary
files by using the in-memory filesystem on
/tmp as the Singularity cache
Building LUMI MPI compatible containers¶
Here we provide an example of building a container that is compatible with the MPI stack on LUMI.
For MPI-enabled containers, the application inside the container must be dynamically linked to an MPI version that is ABI-compatible with the host MPI.
The following Singularity definition file
mpi_osu.def, installs MPICH-3.1.4,
which is ABI-compatible with the Cray-MPICH found on LUMI. That MPICH will be
used to compile the OSU microbenchmarks. Finally, the OSU
point to point bandwidth test is set as the runscript of the image.
bootstrap: docker from: ubuntu:21.04 %post # Install software apt-get update apt-get install -y file g++ gcc gfortran make gdb strace wget ca-certificates --no-install-recommends # Install mpich wget -q http://www.mpich.org/static/downloads/3.1.4/mpich-3.1.4.tar.gz tar xf mpich-3.1.4.tar.gz cd mpich-3.1.4 ./configure --disable-fortran --enable-fast=all,O3 --prefix=/usr make -j$(nproc) make install ldconfig # Build osu benchmarks wget -q http://mvapich.cse.ohio-state.edu/download/mvapich/osu-micro-benchmarks-5.3.2.tar.gz tar xf osu-micro-benchmarks-5.3.2.tar.gz cd osu-micro-benchmarks-5.3.2 ./configure --prefix=/usr/local CC=$(which mpicc) CFLAGS=-O3 make make install cd .. rm -rf osu-micro-benchmarks-5.3.2 rm osu-micro-benchmarks-5.3.2.tar.gz %runscript /usr/local/libexec/osu-micro-benchmarks/mpi/pt2pt/osu_bw
The image can be built on your local hardware (not LUMI) with